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Cooke Mol.Gen. (2004)

Morse, A.M., Cooke, J.E.K., and Davis, J.M. 2004. Functional genomics in forest trees.  Chapter 1 in: Molecular Genetics and Breeding of Forest Trees. S. Kumar and M. Fladung, eds. Haworth Press, New York.  462 pp.

Copyright 2004, Haworth Press Inc., New York NY, Functional genomics in forest trees, Chapter 1 in: Molecular Genetics and Breeding of Forest Trees, 462 pp. Article copies available from The Haworth Document Delivery Service : 1-800-HAWORTH or


Genomic science has revolutionized how gene function is studied.  Scientists have unprecedented access to gene sequence information, in some cases to the entire genome sequence.  This information has motivated new perspectives and approaches to carrying out biological research on many different organisms, including forest trees.  Forest tree functional genomics aims to define the roles played by all of the genes in a tree.  The accomplishment of this aim will indeed be a challenge, however along the way experiments are sure to reveal novel and unexpected aspects of tree biology.  Furthermore, it seems likely that forest tree functional genomics will lead to new insights on manipulating tree genomes for practical benefits such as increasing yield or altering wood quality.

Prior to the genomics era, scientists were technologically restricted to identifying and characterizing one or a few genes at a time.  Often, these genes were identified as important because they encoded proteins that were abundant or that exhibited a particular enzyme activity.  Characterization was much more difficult for genes that encoded proteins of low abundance, or with transitory, ill-defined or completely unknown activities.  Consequently, many genes were not studied.  For example, genes encoding proteins involved in signal transduction – the process of coordinating growth, development, and environmental responsiveness – remained poorly understood because these proteins tend to be of low abundance and have activities that are transitory and /or poorly defined.  Another difficulty associated with the “one-gene-at-a-time” approach is that it is not obvious how any one gene fits into the bigger picture of cellular and organismal processes.  Today, scientists can query an organism via a genomics approach and identify the genes and proteins with potential roles in a process of interest, without any a priori knowledge of function.  The comprehensive picture of an organism that is afforded by functional genomics has changed the way we approach biological research.  This is because the analytical tools at our disposal to observe levels of mRNA, proteins and metabolites, and their interactions provide global phenotyping information.

There are many different interpretations of the phrase “functional genomics” currently in use in the scientific community (Hieter & Boguski, 1997).  In this chapter we define functional genomics as the analysis of the roles played by all of the genes in an organism, typically involving high-throughput experiments that generate large quantities of information.  There are a number of research areas associated with functional genomics, including proteomics and metabolomics, that are beyond the scope of this chapter.  Consequently, we will primarily discuss the analysis of mRNA expression abundance, i.e., analysis of the transcriptome.  This chapter introduces some concepts of functional genomics, with particular reference to its use in understanding forest trees.  Because the cornerstone of functional genomics is the sequence information contained in genes, we will first discuss methods that have been used to discover and sequence tree genes.  We then discuss two key papers from work in yeast and Arabidopsis thaliana that help define the potential roles of genetic manipulation and microarrays in forest tree functional genomics.  Finally, we turn to biological features of forest trees that make them unique among plants, and also affect the kinds of functional genomics approaches that are most likely to be successful.